If you taxed churches, wouldn't you have to tax all non-profit institutions? The reason churches are tax-exempt isn't because they're religious organizations, it's because they meet the definition of non-profit organizations under IRS rules.
I agree but disagree. Catholic Church, Protestant churches, etc should not be taxed but cults like scientology or Jehovah witnesses should be taxed (well their not legit).
And there we have the problem. Say what you like about the Jehovah's, they are a legitimate religious organisation with a grand tradition. Who is to describe what is a "cult" and what is a "religion"?
Cults are the ones we don't like, you see.